Chapter 14: Genomes and Genomics

What is a genome

The complete set of DNA in a single cell of an organism

What was the human genome project

Allows for the identification of disease genes and the development of new treatment strategies

When was the first draft of human genome

2001- 3000 MB first draft

What was teh structure of the human genome project

A coordinated effort to sequence and identify all genes of human genome in order to make a reference genome

What is forward vs reverse genetics

Forward genetics starts with a mutant phenotype (an observed change) and works to identify the gene (genotype) responsible for that change. Conversely, reverse genetics starts with a known gene (genotype) and specifically alters it to study the resulting phenotype (function).

What is sequence assembly of genomes

Building up all fo the individual reads into a consensus sequences that is an authentic representation for each of the DNA molecules

What are the four steps to obtaining the swurnce of a genome

1. Break the genome up into thousands to millions of more or less random little pieces

2. Read the sequence of each little piece

3. Overlap the little pieces where their sequences are identical

4. Continue overlapping ever-larger pieces until you’ve accounted from all the little pieces

Sequences of overlapping reads are assembled into unites called_____ ____. That are sequences that are contiguous or touching

Sequence contigs

To obtain and assemble the sequence of a genome use

Whole genome shotgun sequencing

What are the two methods of white genome shotgun sequencing

1. traditional: whole-genome shotgun gun sequencing

2. Next generation whole-genome shotgun sequencing

Why is whole g4enome shotgun sequencing called shotgun

Sequence reads are obtained randomly from the whole genome without any information on where in the genome they came from

What are the three steps to next generations WGS

Obtain a large # of overlapping sequences that can be assembled into contigs

1. DNA molecules must be prepared for sequencing in cell free reactions, without cloning in microbial reaction

2. Millions of individual DNA fragments are isolated and sequenced in parallel during each machine run

3. Advanced fluid handling technologies, cameras, and softwares make it possible to detect the products of sequencing reactions in small reaction volumes

When and why was next generation WGS made

Started after the human genome project, it is a faster and cheaper way of sequencing

In illumina sequencing what happens

Illumina sequencing breaks DNA into millions of tiny pieces, attaches them to a slide, and then clones each piece into clusters. The process adds colored DNA one at a time, with a chemical stop that allows a camera to record rhe color added to every cluster. By repeating this process, the machine can read the entire sequence.

How does illumina sequencing differ from Sanger sequencing

All the nucleotides are chain terminating meaning there are no normal dNTPs

Compare Sanger decoy and illumina

Sanger: adds a H, irreversible terminating group

Illumina: adds an OR, reversible terminating group

What are pacific biosciences ?

These are machine sequences that have very long DNA sequences with average lengths reading over 10,000 bases. They are useful for assembling new genomes, they can also detect methylation of DNA strands

What aer Oxford nano pore technologies?

They are capable of sequencing trace amounts of DNA, PCR is not required, they long read 10-100kb, and ultra long read 100-300 kb. They are small enough to fit in ones pocket and is used in field development such as Zika monitoring in Brazil

In Oxford nanopore technology

1. The enzyme unwinds DNA, and feeds 1 strand thru protein pore

2. Then a unique shape of each DNA causes characteristics disruption in electrical currrent

3. Sequence is read

Why is whole genome sequence assembly difficult (4)

1. Challenge is to assemble the contigs into the entire gemnome sequence

2. Difficulty is due to size and complexity of the genome

3. Eukaryotic chromosomes include a variety of repetitive dna segments

4. Difffiuclt to align as sequence reads

What are the two strategies for whole genome shotgun sequencing assembly

1. First the unique sequence overlaps between the sequence reads are used to build contigs

2. Then the pair ends reads and are then used to span gaps and to order/orient contigs into large units called scaffolds

What are bioinformatics

The analysis of the entire genomic sequence for informational content

What is comparative genomics

Considers the genomes of closely and distantly relates species for evolutionary insight

What is functional genomics

Functional genomics is the uses an expanding variety of methods to study function, expression and interaction of gene products

What is included in bioinformatics

The information content of the genome, sum of all sequences that encode proteins, RNA plus binding sites in DNA and mRNA

What is annotation

Process of identifying genes, their regulatory sequences and their functions

What are the 5 approaches for deducing the polypeptides

1. ORF detection

2. Direct evidence from cDNA sequences

3. Predictions of binding sites

4. Using polypeptide and DNA similarity

5. Predictions based on codon bias

What is open reading frame detection

Computer scans DNA sequences of both strands in each reading frame, there are 3 possible reading frames on each strands with a total of 6 reading frames total. They loook for gene size, start and stop codons

What is direct evidence from cDNA sequences (through the analysis of mRNA)

In cDNA< open reading frames should be continuous from initiation codon through the stop codon . Thus cDNA sequences can greatly assist in identifying correct reading frames, including initiation and stop codons

What are predictions of binding sites

Basically, “gene finding” computer programs search for predicate sequences such as the TATA box, ttranslation start and stop codons, and 5’3 splice sites

What are using polypeptide and dna similarity used for

This includes the blast tool in which a sequence can be submitted as a nucleotide sequence or a protein sequence. With this tool the computer can analyze if there are close matches to this sequence since many ancestors share simiar genes

What are synonymous codons

When there are mutliple codons for a single amino acid

In fruit flies, for two codons for cysteine

UGC is used 73% of the time

UGU is used 27% of the time

What is comparative genomics and what two things does it reveal

Comparative genomics considers genomes of closely and distantly related species for evolutionary insight, and they are used to identify conserved regions, and to reveal how species diverge

What are 5 things comparative genomics looks for

1. Sequence similarity

2. Gene location

3. Length and number of coding regions

4. Amount of noncoding DNA

5. Highly conserved regions

What is phylogenetic

The study of evolutionary relationships

What is a phylogeny

Relationship between organisms w a common ancestor

What is the phylogenetic tree

A graph representing evolutionary hisotry of sequencies/species

What are the two steps of comparative genomics

Step 1. Decide which species genomes to compare

Step 2: identify rhe most related genes called homologs

Genes that are homologs can be recognized by similarities in their

DNA sequences and the amino acid sequences of proteins they encode

What are the two types of gene homologs

1. Orthologs

2. Paralogs

What are orthologs

Homologs include genes in different species that evolved from a common ancestral gene. They usually retain the same function

Paralogs

Are genes related by duplication within the genome. They usually evolve new functions which may be related to the original function

What are monotremes ?

They lay eggs.

Platypus genome has

One egg yolk gene called vitellogenin

Anaylsis of ____ and _____ genomes revealed no such functional yolk genes

Marsupial

Eutherian

Presence of vitellogenin in platypus and its absence from other mammals is examples in two ways

1. Vitellogenin is a novel invention

2. Vitellogenin existed in a common ancestor

When studying infrequency events such as the invention of a gene, evolutionary biologists prefer to rely on the principle of

Parsimony

What is Ockham’s Razor

Out of the two competitions explanations, the simpler should be proffered

The human genome carries relics of egg laying ancestors known as

Yolk pseudogenes

Compare homologs between mice and humans

99% have some homologs similar

Human posses one adidtionalparalog of opsin known as

Color vision

Mice have more genes in relation with

Olfaction genes

Most of human sequence variants are common variants, also called _______ and most of them are

Polymorphisms, one nucleotide, single nucleoside polymorphisms

Any 2 unrelated human genomes are how much identical

99.9%

Rare variants found in genomes are restricted to

Cleosly related populations or families

What is genome wide association studies

Common variants used as genetic markers and asosciatons are analyzed. Correlation does not indicate causal gene

Humans differ in the ____ ____ _____ of parts of individual genes, entire genes or sets of gene

Number of copies (copy number variations) for example people w high starch diets have more copies of salivary amylase gene

What are functional genomics

The study of function expression and interactions of gene products

What is trasncriptome

Sequence and expression patterns of all RNA transcripts

What are proteome

Sequence and expression patterns of all proteins

What are interactive

Complete set of physical interactions between proteins and DNA segments, between proteins and RNA segments, and between proteins